Receptor
PDB id Resolution Class Description Source Keywords
3V7Y 1.97 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH 5'-N-PROPARGYLAMINO-5'-DEOXYADENOSINE LISTERIA MONOCYTOGENES LIGAND-SCREENING BY CRYSTALLOGRAPHY TWO-DOMAIN KINASE INORPOLYPHOSPHATE/ATP-NAD KINASE 1 TRANSFERASE
Ref.: SCREENING AND IN SITU SYNTHESIS USING CRYSTALS OF A KINASE LEAD TO A POTENT ANTISTAPHYLOCOCCAL COMPOUND STRUCTURE V. 20 1107 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A3N A:302;
A:303;
Valid;
Valid;
none;
none;
submit data
304.305 C13 H16 N6 O3 C#CCN...
CIT A:301;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DHU 2.33 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH A NOVEL INHIBITOR LISTERIA MONOCYTOGENES SEROVAR 1/2A (SATCC BAA-679 / EGD-E) TETRAMERIC NAD KINASE TRANSFERASE
Ref.: 8-THIOALKYL-ADENOSINE DERIVATIVES INHIBIT LISTERIA MONOCYTOGENES NAD KINASE THROUGH A NOVEL BINDING MO EUR.J.MED.CHEM. V. 124 1041 2016
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A3N; Similar ligands found: 228
No: Ligand ECFP6 Tc MDL keys Tc
1 A3N 1 1
2 XYA 0.651515 0.923077
3 ADN 0.651515 0.923077
4 RAB 0.651515 0.923077
5 AOC 0.64 0.924242
6 5N5 0.632353 0.953125
7 A4D 0.623188 0.923077
8 5CD 0.623188 0.878788
9 EP4 0.597222 0.869565
10 DTA 0.589041 0.828571
11 M2T 0.589041 0.819444
12 3DH 0.586667 0.867647
13 6RE 0.584416 0.821918
14 MTA 0.581081 0.867647
15 A 0.571429 0.783784
16 LMS 0.571429 0.690476
17 AMP 0.571429 0.783784
18 J7C 0.56962 0.833333
19 SRA 0.564103 0.74359
20 GJV 0.5625 0.810811
21 ZAS 0.551282 0.830986
22 5AD 0.550725 0.815385
23 ABM 0.55 0.763158
24 A2D 0.55 0.786667
25 5AS 0.548781 0.689655
26 DSH 0.5375 0.859155
27 BA3 0.536585 0.786667
28 AP2 0.536585 0.75641
29 A12 0.536585 0.75641
30 AU1 0.535714 0.766234
31 AP5 0.53012 0.786667
32 ADP 0.53012 0.786667
33 B4P 0.53012 0.786667
34 S4M 0.52439 0.782051
35 SON 0.52381 0.734177
36 AT4 0.52381 0.75641
37 AN2 0.52381 0.776316
38 MAO 0.518072 0.75
39 ADX 0.517647 0.710843
40 CA0 0.517647 0.766234
41 MHZ 0.517647 0.772152
42 M33 0.517647 0.776316
43 ATP 0.511628 0.786667
44 50T 0.511628 0.776316
45 HEJ 0.511628 0.786667
46 ACP 0.511628 0.766234
47 SFG 0.511628 0.814286
48 G5A 0.511364 0.689655
49 A7D 0.505882 0.869565
50 AQP 0.505747 0.786667
51 PRX 0.505747 0.74359
52 5FA 0.505747 0.786667
53 APC 0.505747 0.75641
54 AR6 0.505747 0.786667
55 APR 0.505747 0.786667
56 ANP 0.505618 0.766234
57 RBY 0.5 0.75641
58 SAP 0.5 0.746835
59 ADV 0.5 0.75641
60 ADP PO3 0.5 0.783784
61 AD9 0.5 0.766234
62 AGS 0.5 0.746835
63 Y3J 0.5 0.791045
64 7D7 0.5 0.808824
65 8X1 0.494624 0.666667
66 A5A 0.494505 0.674419
67 5X8 0.494253 0.855072
68 VO4 ADP 0.48913 0.753247
69 ADP VO4 0.48913 0.753247
70 SSA 0.48913 0.689655
71 TAT 0.488889 0.75641
72 T99 0.488889 0.75641
73 GAP 0.488889 0.789474
74 ACQ 0.488889 0.766234
75 52H 0.483871 0.651685
76 54H 0.483871 0.659091
77 VMS 0.483871 0.659091
78 5AL 0.483516 0.753247
79 SA8 0.483146 0.810811
80 A5D 0.483146 0.828571
81 A3G 0.481928 0.897059
82 NEC 0.481928 0.865672
83 3AM 0.481481 0.77027
84 MAP 0.478723 0.746835
85 TSB 0.478723 0.686047
86 53H 0.478723 0.651685
87 5CA 0.478723 0.689655
88 ATF 0.478261 0.75641
89 ALF ADP 0.478261 0.725
90 ADP ALF 0.478261 0.725
91 SAI 0.477778 0.819444
92 SAH 0.477778 0.830986
93 OOB 0.473684 0.753247
94 9ZD 0.473684 0.716049
95 9ZA 0.473684 0.716049
96 S7M 0.473118 0.766234
97 6YZ 0.473118 0.766234
98 SRP 0.473118 0.75641
99 SAM 0.472527 0.766234
100 P5A 0.469388 0.659341
101 4AD 0.46875 0.746835
102 ADQ 0.46875 0.789474
103 0UM 0.46875 0.8
104 NSS 0.46875 0.670455
105 DSZ 0.46875 0.670455
106 LSS 0.46875 0.637363
107 EEM 0.467391 0.766234
108 AAT 0.467391 0.835616
109 00A 0.463918 0.716049
110 NVA LMS 0.463918 0.630435
111 DLL 0.463918 0.753247
112 AHX 0.463918 0.75
113 DAL AMP 0.463158 0.753247
114 A22 0.463158 0.776316
115 LEU LMS 0.459184 0.630435
116 ADP BMA 0.459184 0.789474
117 5SV 0.458333 0.707317
118 8QN 0.458333 0.753247
119 25A 0.458333 0.763158
120 S8M 0.458333 0.797297
121 SMM 0.457447 0.7375
122 B5V 0.454545 0.734177
123 A3S 0.454545 0.882353
124 GSU 0.454545 0.651685
125 A A 0.454545 0.763158
126 3AD 0.454545 0.878788
127 KAA 0.454545 0.666667
128 A3R 0.453608 0.782051
129 A1R 0.453608 0.782051
130 AMO 0.453608 0.75641
131 PAJ 0.453608 0.740741
132 2AM 0.451219 0.783784
133 B5M 0.45098 0.725
134 YLA 0.45045 0.746988
135 JB6 0.45 0.716049
136 NB8 0.45 0.728395
137 PTJ 0.45 0.707317
138 TXA 0.45 0.75641
139 BIS 0.45 0.7375
140 8Q2 0.449541 0.685393
141 A3P 0.448276 0.76
142 YSA 0.446602 0.651685
143 OAD 0.444444 0.766234
144 A3T 0.444444 0.895522
145 9X8 0.444444 0.746835
146 3UK 0.444444 0.74359
147 GEK 0.443299 0.797297
148 4UV 0.442308 0.746835
149 AMP DBH 0.442308 0.766234
150 LAD 0.44 0.740741
151 CC5 0.44 0.863636
152 PR8 0.44 0.731707
153 WAQ 0.44 0.716049
154 7D5 0.439024 0.727273
155 FA5 0.436893 0.734177
156 8PZ 0.436893 0.670455
157 YAP 0.436893 0.725
158 3OD 0.435644 0.766234
159 9K8 0.435644 0.630435
160 SXZ 0.435644 0.766234
161 1ZZ 0.435644 0.682353
162 ME8 0.435644 0.702381
163 FYA 0.435644 0.753247
164 OVE 0.435294 0.753247
165 62X 0.434343 0.759494
166 4UU 0.433962 0.746835
167 XAH 0.432692 0.722892
168 MYR AMP 0.431373 0.682353
169 25L 0.431373 0.776316
170 A6D 0.43 0.734177
171 K15 0.43 0.779221
172 QQX 0.428571 0.705128
173 9SN 0.427184 0.707317
174 ACK 0.423529 0.753425
175 RP1 0.423529 0.717949
176 SP1 0.423529 0.717949
177 QQY 0.423529 0.714286
178 ATP A A A 0.423077 0.773333
179 B5Y 0.423077 0.725
180 YLP 0.422018 0.705882
181 BS5 0.421053 0.67033
182 AFH 0.420561 0.740741
183 ARG AMP 0.420561 0.714286
184 7MD 0.420561 0.743902
185 PAP 0.419355 0.773333
186 D3Y 0.418367 0.857143
187 NAI 0.418182 0.759494
188 4UW 0.418182 0.719512
189 3L1 0.417722 0.84058
190 MTP 0.417722 0.791667
191 3D1 0.417722 0.84058
192 KB1 0.417476 0.8
193 KH3 0.416667 0.792208
194 4YB 0.416667 0.637363
195 2BA 0.41573 0.756757
196 CMP 0.41573 0.767123
197 A2P 0.41573 0.746667
198 TYR AMP 0.415094 0.725
199 AF3 ADP 3PG 0.414414 0.698795
200 2VA 0.413043 0.869565
201 AHZ 0.412844 0.682353
202 6MD 0.4125 0.880597
203 26A 0.4125 0.855072
204 2FA 0.4125 0.857143
205 7C5 0.411215 0.763158
206 G3A 0.411215 0.728395
207 AP0 0.410714 0.75
208 YLB 0.410714 0.705882
209 YLC 0.410714 0.743902
210 48N 0.409091 0.728395
211 G5P 0.407407 0.728395
212 GA7 0.407407 0.779221
213 AR6 AR6 0.407407 0.763158
214 5F1 0.407407 0.771429
215 PPS 0.40625 0.690476
216 DND 0.405405 0.75641
217 NXX 0.405405 0.75641
218 7D3 0.404494 0.730769
219 NVA 2AD 0.404255 0.821918
220 TAD 0.40367 0.719512
221 GTA 0.40367 0.702381
222 DQV 0.40367 0.776316
223 IOT 0.403509 0.697674
224 WSA 0.401786 0.659091
225 649 0.401786 0.623656
226 LAQ 0.4 0.682353
227 VRT 0.4 0.833333
228 SO8 0.4 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5dhu.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5dhu.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
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